pub struct HomopolyPairHMM { /* private fields */ }Expand description
A pair Hidden Markov Model for comparing sequences x and y as described by Durbin, R., Eddy, S., Krogh, A., & Mitchison, G. (1998). Biological Sequence Analysis. Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492. The default model has been extended to consider homopolymer errors, at the cost of more states and transitions.
Implementations
sourceimpl HomopolyPairHMM
impl HomopolyPairHMM
sourcepub fn new<G, H>(gap_params: &G, hop_params: &H) -> Self where
G: GapParameters,
H: HopParameters,
pub fn new<G, H>(gap_params: &G, hop_params: &H) -> Self where
G: GapParameters,
H: HopParameters,
Create a new instance of a HomopolyPairHMM.
Arguments
gap_params- parameters for opening or extending gapshop_params- parameters for opening or extending hops
Calculate the probability of sequence x being related to y via any alignment.
Arguments
emission_params- parameters for emissionalignment_mode- parameters for free end/start gapsmax_edit_dist- maximum edit distance to consider; if notNone, perform banded alignment
Trait Implementations
sourceimpl Clone for HomopolyPairHMM
impl Clone for HomopolyPairHMM
sourcefn clone(&self) -> HomopolyPairHMM
fn clone(&self) -> HomopolyPairHMM
Returns a copy of the value. Read more
1.0.0 · sourcefn clone_from(&mut self, source: &Self)
fn clone_from(&mut self, source: &Self)
Performs copy-assignment from source. Read more
Auto Trait Implementations
impl RefUnwindSafe for HomopolyPairHMM
impl Send for HomopolyPairHMM
impl Sync for HomopolyPairHMM
impl Unpin for HomopolyPairHMM
impl UnwindSafe for HomopolyPairHMM
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcepub fn borrow_mut(&mut self) -> &mut T
pub fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
impl<SS, SP> SupersetOf<SS> for SP where
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SP where
SS: SubsetOf<SP>,
pub fn to_subset(&self) -> Option<SS>
pub fn to_subset(&self) -> Option<SS>
The inverse inclusion map: attempts to construct self from the equivalent element of its
superset. Read more
pub fn is_in_subset(&self) -> bool
pub fn is_in_subset(&self) -> bool
Checks if self is actually part of its subset T (and can be converted to it).
pub fn to_subset_unchecked(&self) -> SS
pub fn to_subset_unchecked(&self) -> SS
Use with care! Same as self.to_subset but without any property checks. Always succeeds.
pub fn from_subset(element: &SS) -> SP
pub fn from_subset(element: &SS) -> SP
The inclusion map: converts self to the equivalent element of its superset.
sourceimpl<T> ToOwned for T where
T: Clone,
impl<T> ToOwned for T where
T: Clone,
type Owned = T
type Owned = T
The resulting type after obtaining ownership.
sourcepub fn to_owned(&self) -> T
pub fn to_owned(&self) -> T
Creates owned data from borrowed data, usually by cloning. Read more
sourcepub fn clone_into(&self, target: &mut T)
pub fn clone_into(&self, target: &mut T)
toowned_clone_into)Uses borrowed data to replace owned data, usually by cloning. Read more